Multiple sequence alignment - TraesCS5D01G041300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G041300 chr5D 100.000 3530 0 0 1 3530 41879445 41875916 0.000000e+00 6519.0
1 TraesCS5D01G041300 chr5B 97.888 1231 22 1 1274 2500 36554582 36553352 0.000000e+00 2126.0
2 TraesCS5D01G041300 chr5B 95.807 787 28 4 595 1379 36558152 36557369 0.000000e+00 1266.0
3 TraesCS5D01G041300 chr5B 94.281 647 25 9 2612 3252 36553355 36552715 0.000000e+00 979.0
4 TraesCS5D01G041300 chr5B 91.667 624 19 8 3 602 36567114 36566500 0.000000e+00 833.0
5 TraesCS5D01G041300 chr5B 85.502 269 29 4 79 339 41265950 41265684 4.490000e-69 272.0
6 TraesCS5D01G041300 chr5B 95.041 121 6 0 2495 2615 71643799 71643679 1.290000e-44 191.0
7 TraesCS5D01G041300 chr2B 78.769 1300 195 51 1005 2274 785984550 785983302 0.000000e+00 797.0
8 TraesCS5D01G041300 chr2B 80.718 529 89 9 1010 1534 775385755 775386274 1.970000e-107 399.0
9 TraesCS5D01G041300 chr2B 94.915 118 6 0 2498 2615 762215934 762215817 6.020000e-43 185.0
10 TraesCS5D01G041300 chr2B 82.955 176 28 2 725 900 198947009 198947182 1.310000e-34 158.0
11 TraesCS5D01G041300 chr6D 74.741 1255 260 42 1018 2248 426109778 426108557 3.140000e-140 508.0
12 TraesCS5D01G041300 chr6D 92.188 128 9 1 2487 2614 329858584 329858710 2.800000e-41 180.0
13 TraesCS5D01G041300 chr6B 74.740 1251 258 43 1018 2248 641405040 641403828 1.130000e-139 507.0
14 TraesCS5D01G041300 chr6B 93.893 131 7 1 2496 2626 457400728 457400599 2.780000e-46 196.0
15 TraesCS5D01G041300 chr1B 73.815 1287 271 49 1010 2275 592367225 592365984 1.930000e-122 449.0
16 TraesCS5D01G041300 chr1B 80.822 511 88 8 1017 1525 9647386 9647888 3.300000e-105 392.0
17 TraesCS5D01G041300 chr1B 94.958 119 5 1 2496 2614 591426329 591426212 6.020000e-43 185.0
18 TraesCS5D01G041300 chr1B 83.784 185 28 2 720 904 32368099 32368281 1.300000e-39 174.0
19 TraesCS5D01G041300 chr5A 84.424 443 51 6 76 510 689900248 689900680 1.520000e-113 420.0
20 TraesCS5D01G041300 chr4A 83.585 463 57 7 58 510 656482899 656482446 1.960000e-112 416.0
21 TraesCS5D01G041300 chr2D 81.285 529 86 11 1010 1534 631983068 631983587 1.960000e-112 416.0
22 TraesCS5D01G041300 chr2D 92.188 128 9 1 2487 2614 305940129 305940255 2.800000e-41 180.0
23 TraesCS5D01G041300 chr2D 81.915 188 32 2 720 907 609284422 609284237 1.310000e-34 158.0
24 TraesCS5D01G041300 chr1D 75.079 955 203 29 1030 1971 437292978 437292046 2.540000e-111 412.0
25 TraesCS5D01G041300 chr1D 81.250 512 82 11 1017 1524 7372042 7372543 5.490000e-108 401.0
26 TraesCS5D01G041300 chr1A 81.445 512 83 11 1017 1525 9533045 9532543 3.280000e-110 409.0
27 TraesCS5D01G041300 chr7B 95.122 123 6 0 2495 2617 517095192 517095070 1.000000e-45 195.0
28 TraesCS5D01G041300 chr7B 100.000 34 0 0 3264 3297 184298907 184298874 2.940000e-06 63.9
29 TraesCS5D01G041300 chr3D 86.517 178 22 2 3354 3530 614464487 614464311 1.000000e-45 195.0
30 TraesCS5D01G041300 chr3D 82.011 189 31 3 724 911 325026101 325025915 1.310000e-34 158.0
31 TraesCS5D01G041300 chr4B 94.215 121 7 0 2498 2618 143310081 143309961 6.020000e-43 185.0
32 TraesCS5D01G041300 chr3B 94.215 121 7 0 2494 2614 172008614 172008734 6.020000e-43 185.0
33 TraesCS5D01G041300 chr7D 83.060 183 30 1 725 907 160536064 160535883 7.840000e-37 165.0
34 TraesCS5D01G041300 chr7D 82.584 178 30 1 725 902 41570080 41570256 4.720000e-34 156.0
35 TraesCS5D01G041300 chr3A 82.258 186 30 2 724 907 99589504 99589320 1.310000e-34 158.0
36 TraesCS5D01G041300 chrUn 81.283 187 33 2 725 910 89020693 89020878 2.200000e-32 150.0
37 TraesCS5D01G041300 chr7A 100.000 34 0 0 3264 3297 229143716 229143749 2.940000e-06 63.9


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G041300 chr5D 41875916 41879445 3529 True 6519 6519 100.000 1 3530 1 chr5D.!!$R1 3529
1 TraesCS5D01G041300 chr5B 36552715 36558152 5437 True 1457 2126 95.992 595 3252 3 chr5B.!!$R4 2657
2 TraesCS5D01G041300 chr5B 36566500 36567114 614 True 833 833 91.667 3 602 1 chr5B.!!$R1 599
3 TraesCS5D01G041300 chr2B 785983302 785984550 1248 True 797 797 78.769 1005 2274 1 chr2B.!!$R2 1269
4 TraesCS5D01G041300 chr2B 775385755 775386274 519 False 399 399 80.718 1010 1534 1 chr2B.!!$F2 524
5 TraesCS5D01G041300 chr6D 426108557 426109778 1221 True 508 508 74.741 1018 2248 1 chr6D.!!$R1 1230
6 TraesCS5D01G041300 chr6B 641403828 641405040 1212 True 507 507 74.740 1018 2248 1 chr6B.!!$R2 1230
7 TraesCS5D01G041300 chr1B 592365984 592367225 1241 True 449 449 73.815 1010 2275 1 chr1B.!!$R2 1265
8 TraesCS5D01G041300 chr1B 9647386 9647888 502 False 392 392 80.822 1017 1525 1 chr1B.!!$F1 508
9 TraesCS5D01G041300 chr2D 631983068 631983587 519 False 416 416 81.285 1010 1534 1 chr2D.!!$F2 524
10 TraesCS5D01G041300 chr1D 437292046 437292978 932 True 412 412 75.079 1030 1971 1 chr1D.!!$R1 941
11 TraesCS5D01G041300 chr1D 7372042 7372543 501 False 401 401 81.250 1017 1524 1 chr1D.!!$F1 507
12 TraesCS5D01G041300 chr1A 9532543 9533045 502 True 409 409 81.445 1017 1525 1 chr1A.!!$R1 508

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
960 987 0.391661 ATCGTTCTGCGCATCAGGTT 60.392 50.0 12.24 0.0 43.06 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2739 5707 0.322008 CTCCTCCAGTGTTCCCTTGC 60.322 60.0 0.0 0.0 0.0 4.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
145 146 1.377536 GACAGAAGGCCTCATTGAGC 58.622 55.000 5.23 4.12 0.00 4.26
198 203 0.723981 GTTCTTGGCGTCATCTCAGC 59.276 55.000 0.00 0.00 0.00 4.26
207 212 2.674852 GCGTCATCTCAGCATTCTCAAA 59.325 45.455 0.00 0.00 0.00 2.69
211 216 5.106791 CGTCATCTCAGCATTCTCAAAAACT 60.107 40.000 0.00 0.00 0.00 2.66
276 281 1.228154 GGGTTGTTTCCTCCGCAGT 60.228 57.895 0.00 0.00 0.00 4.40
307 319 2.823154 AGATGCGTATAGAGCCTCTTCC 59.177 50.000 0.00 0.00 36.44 3.46
309 321 1.681793 TGCGTATAGAGCCTCTTCCAC 59.318 52.381 0.00 0.00 0.00 4.02
359 371 2.138320 CACGTTGCAGATCTTGTCACT 58.862 47.619 0.00 0.00 0.00 3.41
360 372 2.545526 CACGTTGCAGATCTTGTCACTT 59.454 45.455 0.00 0.00 0.00 3.16
361 373 2.545526 ACGTTGCAGATCTTGTCACTTG 59.454 45.455 0.00 0.00 0.00 3.16
362 374 2.545526 CGTTGCAGATCTTGTCACTTGT 59.454 45.455 0.00 0.00 0.00 3.16
363 375 3.740832 CGTTGCAGATCTTGTCACTTGTA 59.259 43.478 0.00 0.00 0.00 2.41
364 376 4.389992 CGTTGCAGATCTTGTCACTTGTAT 59.610 41.667 0.00 0.00 0.00 2.29
365 377 5.625251 GTTGCAGATCTTGTCACTTGTATG 58.375 41.667 0.00 0.00 0.00 2.39
366 378 4.256110 TGCAGATCTTGTCACTTGTATGG 58.744 43.478 0.00 0.00 0.00 2.74
376 388 4.000988 GTCACTTGTATGGTTGTACCCTG 58.999 47.826 0.00 0.00 37.50 4.45
405 417 2.180276 ACCAAACCTCTCTCGCATAGT 58.820 47.619 0.00 0.00 0.00 2.12
438 450 2.016318 TGATATGCTCCGCTGTTTTGG 58.984 47.619 0.00 0.00 0.00 3.28
440 452 1.312371 TATGCTCCGCTGTTTTGGGC 61.312 55.000 0.00 0.00 0.00 5.36
454 466 2.123248 TTGGGCTCCTGATCGCACAA 62.123 55.000 4.14 4.14 46.32 3.33
462 474 1.061131 CCTGATCGCACAATCGACAAC 59.939 52.381 0.00 0.00 41.62 3.32
532 557 9.717942 CCAAACTTGCTAGCTATATATTTCTCT 57.282 33.333 17.23 0.00 0.00 3.10
628 653 6.248569 TGTTCAGGAAGTTTTACCTCTCTT 57.751 37.500 0.00 0.00 33.91 2.85
670 695 2.521105 AGTCCGTTACAAAAGCTCGT 57.479 45.000 0.00 0.00 0.00 4.18
764 789 2.614057 GCTATGACAAAATAGCGTGGCT 59.386 45.455 0.80 0.00 44.04 4.75
771 796 5.239744 TGACAAAATAGCGTGGCTCTTAAAA 59.760 36.000 0.00 0.00 40.44 1.52
788 813 7.429636 TCTTAAAATACGCTTTTAGTGTGCT 57.570 32.000 3.30 0.00 39.60 4.40
883 908 1.162698 AGCGTACTGTTAGCGACTCA 58.837 50.000 0.00 0.00 35.78 3.41
946 973 3.869246 CCCGCAGTGAACTTATTATCGTT 59.131 43.478 0.00 0.00 0.00 3.85
960 987 0.391661 ATCGTTCTGCGCATCAGGTT 60.392 50.000 12.24 0.00 43.06 3.50
996 1023 3.643792 AGGCTAATCAACGGAAGCTCTAT 59.356 43.478 0.00 0.00 35.30 1.98
1249 1279 4.164221 ACATACCAAGGAGAACCCATACAG 59.836 45.833 0.00 0.00 37.41 2.74
1520 4442 4.027437 TGTGGAAACCTTAAAAGCCTTGT 58.973 39.130 0.00 0.00 0.00 3.16
1590 4524 2.378038 GGCTATCCTGGCATTGTTTCA 58.622 47.619 0.00 0.00 0.00 2.69
1601 4535 2.097142 GCATTGTTTCAGCTGCTCTAGG 59.903 50.000 9.47 2.01 0.00 3.02
1710 4659 2.094100 TGGTCAGGGAGATGAGGATC 57.906 55.000 0.00 0.00 0.00 3.36
1891 4840 6.316140 TGACATTGCAATCACCTATTCACTAC 59.684 38.462 9.53 0.00 0.00 2.73
1942 4891 6.946165 TGTTCAATGTTTGTTTTCATGATGC 58.054 32.000 0.00 0.00 0.00 3.91
2007 4956 1.104577 TTGCCGGTTTGTCCTGGTTC 61.105 55.000 1.90 0.00 34.18 3.62
2276 5240 4.377431 CGAGTGTGTTACAAAGGAGATTGC 60.377 45.833 0.00 0.00 33.52 3.56
2317 5281 7.699566 AGTAATGAAAGAGAGACGACATAGAC 58.300 38.462 0.00 0.00 0.00 2.59
2413 5381 4.573607 TGAATATTCATGTGCTGACTGAGC 59.426 41.667 14.23 0.00 39.21 4.26
2496 5464 5.551760 GGAAACTGTCCAACTACATGATG 57.448 43.478 0.00 0.00 46.97 3.07
2497 5465 5.003804 GGAAACTGTCCAACTACATGATGT 58.996 41.667 2.65 2.65 46.97 3.06
2498 5466 6.170506 GGAAACTGTCCAACTACATGATGTA 58.829 40.000 5.05 5.05 46.97 2.29
2499 5467 6.092259 GGAAACTGTCCAACTACATGATGTAC 59.908 42.308 0.23 0.00 46.97 2.90
2500 5468 6.360370 AACTGTCCAACTACATGATGTACT 57.640 37.500 0.23 0.00 0.00 2.73
2501 5469 5.967088 ACTGTCCAACTACATGATGTACTC 58.033 41.667 0.23 0.00 0.00 2.59
2502 5470 5.105310 ACTGTCCAACTACATGATGTACTCC 60.105 44.000 0.23 0.00 0.00 3.85
2503 5471 4.161565 TGTCCAACTACATGATGTACTCCC 59.838 45.833 0.23 0.00 0.00 4.30
2504 5472 4.406003 GTCCAACTACATGATGTACTCCCT 59.594 45.833 0.23 0.00 0.00 4.20
2505 5473 4.649674 TCCAACTACATGATGTACTCCCTC 59.350 45.833 0.23 0.00 0.00 4.30
2506 5474 4.202264 CCAACTACATGATGTACTCCCTCC 60.202 50.000 0.23 0.00 0.00 4.30
2507 5475 3.223435 ACTACATGATGTACTCCCTCCG 58.777 50.000 0.23 0.00 0.00 4.63
2508 5476 2.160721 ACATGATGTACTCCCTCCGT 57.839 50.000 0.00 0.00 0.00 4.69
2509 5477 2.467880 ACATGATGTACTCCCTCCGTT 58.532 47.619 0.00 0.00 0.00 4.44
2510 5478 2.431057 ACATGATGTACTCCCTCCGTTC 59.569 50.000 0.00 0.00 0.00 3.95
2511 5479 1.100510 TGATGTACTCCCTCCGTTCG 58.899 55.000 0.00 0.00 0.00 3.95
2512 5480 0.384669 GATGTACTCCCTCCGTTCGG 59.615 60.000 4.74 4.74 0.00 4.30
2513 5481 0.033796 ATGTACTCCCTCCGTTCGGA 60.034 55.000 13.34 13.34 0.00 4.55
2514 5482 0.251297 TGTACTCCCTCCGTTCGGAA 60.251 55.000 14.79 0.04 33.41 4.30
2515 5483 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
2516 5484 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
2517 5485 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2518 5486 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2519 5487 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2520 5488 1.753073 TCCCTCCGTTCGGAATTACTC 59.247 52.381 14.79 0.00 33.41 2.59
2521 5489 1.535437 CCCTCCGTTCGGAATTACTCG 60.535 57.143 14.79 1.97 33.41 4.18
2522 5490 1.133790 CCTCCGTTCGGAATTACTCGT 59.866 52.381 14.79 0.00 33.41 4.18
2523 5491 2.448219 CTCCGTTCGGAATTACTCGTC 58.552 52.381 14.79 0.00 33.41 4.20
2524 5492 1.133025 TCCGTTCGGAATTACTCGTCC 59.867 52.381 11.66 0.00 0.00 4.79
2525 5493 1.135315 CCGTTCGGAATTACTCGTCCA 60.135 52.381 5.19 0.00 33.10 4.02
2526 5494 2.598589 CGTTCGGAATTACTCGTCCAA 58.401 47.619 0.00 0.00 33.10 3.53
2527 5495 3.184541 CGTTCGGAATTACTCGTCCAAT 58.815 45.455 0.00 0.00 33.10 3.16
2528 5496 4.353737 CGTTCGGAATTACTCGTCCAATA 58.646 43.478 0.00 0.00 33.10 1.90
2529 5497 4.799949 CGTTCGGAATTACTCGTCCAATAA 59.200 41.667 0.00 0.00 33.10 1.40
2530 5498 5.289193 CGTTCGGAATTACTCGTCCAATAAA 59.711 40.000 0.00 0.00 33.10 1.40
2531 5499 6.019318 CGTTCGGAATTACTCGTCCAATAAAT 60.019 38.462 0.00 0.00 33.10 1.40
2532 5500 6.838198 TCGGAATTACTCGTCCAATAAATG 57.162 37.500 0.00 0.00 33.10 2.32
2533 5501 6.575267 TCGGAATTACTCGTCCAATAAATGA 58.425 36.000 0.00 0.00 33.10 2.57
2534 5502 7.042950 TCGGAATTACTCGTCCAATAAATGAA 58.957 34.615 0.00 0.00 33.10 2.57
2535 5503 7.713507 TCGGAATTACTCGTCCAATAAATGAAT 59.286 33.333 0.00 0.00 33.10 2.57
2536 5504 7.798516 CGGAATTACTCGTCCAATAAATGAATG 59.201 37.037 0.00 0.00 33.10 2.67
2537 5505 8.621286 GGAATTACTCGTCCAATAAATGAATGT 58.379 33.333 0.00 0.00 33.79 2.71
2543 5511 9.698309 ACTCGTCCAATAAATGAATGTATCTAG 57.302 33.333 0.00 0.00 0.00 2.43
2544 5512 9.914131 CTCGTCCAATAAATGAATGTATCTAGA 57.086 33.333 0.00 0.00 0.00 2.43
2605 5573 8.676454 TTTTTGTGATAAATAATTCCGAACGG 57.324 30.769 6.94 6.94 0.00 4.44
2606 5574 7.612668 TTTGTGATAAATAATTCCGAACGGA 57.387 32.000 12.04 12.04 43.52 4.69
2607 5575 6.838198 TGTGATAAATAATTCCGAACGGAG 57.162 37.500 15.34 0.00 46.06 4.63
2608 5576 5.756347 TGTGATAAATAATTCCGAACGGAGG 59.244 40.000 15.34 0.00 46.06 4.30
2609 5577 5.178809 GTGATAAATAATTCCGAACGGAGGG 59.821 44.000 15.34 0.00 46.06 4.30
2610 5578 3.918294 AAATAATTCCGAACGGAGGGA 57.082 42.857 15.34 2.49 46.06 4.20
2672 5640 4.415501 GCGCGACACAAGTGCTCG 62.416 66.667 12.10 15.68 41.45 5.03
2717 5685 0.608035 AAGGACCGACCGTAACCGTA 60.608 55.000 0.00 0.00 44.74 4.02
2726 5694 3.695816 GACCGTAACCGTAATAGTGTCC 58.304 50.000 0.00 0.00 0.00 4.02
2736 5704 2.358939 AATAGTGTCCGACGTCCAAC 57.641 50.000 10.58 8.94 0.00 3.77
2739 5707 1.663702 GTGTCCGACGTCCAACCAG 60.664 63.158 10.58 0.00 0.00 4.00
2794 5762 1.560923 CGAGGATCCTTGCTTACGTG 58.439 55.000 17.42 0.00 0.00 4.49
2807 5775 3.583276 TACGTGGCCGGCAAGTCAG 62.583 63.158 30.85 14.91 38.78 3.51
2840 5808 0.466007 TGTGGCACAACTGAGCACAT 60.466 50.000 19.74 0.00 44.16 3.21
2885 5853 1.956477 GGTTGTTGATGAGCCAGTGTT 59.044 47.619 0.00 0.00 0.00 3.32
2886 5854 2.030805 GGTTGTTGATGAGCCAGTGTTC 60.031 50.000 0.00 0.00 0.00 3.18
2887 5855 1.896220 TGTTGATGAGCCAGTGTTCC 58.104 50.000 0.00 0.00 0.00 3.62
2890 5858 1.067295 TGATGAGCCAGTGTTCCCTT 58.933 50.000 0.00 0.00 0.00 3.95
2892 5860 0.610232 ATGAGCCAGTGTTCCCTTGC 60.610 55.000 0.00 0.00 0.00 4.01
2893 5861 1.073897 GAGCCAGTGTTCCCTTGCT 59.926 57.895 0.00 0.00 36.26 3.91
2896 5864 0.823356 GCCAGTGTTCCCTTGCTGAA 60.823 55.000 0.00 0.00 0.00 3.02
2899 5867 1.542915 CAGTGTTCCCTTGCTGAATGG 59.457 52.381 0.00 0.00 0.00 3.16
2900 5868 1.145738 AGTGTTCCCTTGCTGAATGGT 59.854 47.619 0.00 0.00 0.00 3.55
2902 5870 3.153919 GTGTTCCCTTGCTGAATGGTAA 58.846 45.455 0.00 0.00 0.00 2.85
2903 5871 3.763897 GTGTTCCCTTGCTGAATGGTAAT 59.236 43.478 0.00 0.00 0.00 1.89
2905 5873 2.917933 TCCCTTGCTGAATGGTAATCG 58.082 47.619 0.00 0.00 0.00 3.34
2906 5874 2.238646 TCCCTTGCTGAATGGTAATCGT 59.761 45.455 0.00 0.00 0.00 3.73
2907 5875 3.452990 TCCCTTGCTGAATGGTAATCGTA 59.547 43.478 0.00 0.00 0.00 3.43
2908 5876 3.560068 CCCTTGCTGAATGGTAATCGTAC 59.440 47.826 0.00 0.00 0.00 3.67
2909 5877 4.188462 CCTTGCTGAATGGTAATCGTACA 58.812 43.478 0.00 0.00 31.21 2.90
2910 5878 4.034048 CCTTGCTGAATGGTAATCGTACAC 59.966 45.833 0.00 0.00 31.21 2.90
2911 5879 4.465632 TGCTGAATGGTAATCGTACACT 57.534 40.909 0.00 0.00 31.21 3.55
2912 5880 5.585820 TGCTGAATGGTAATCGTACACTA 57.414 39.130 0.00 0.00 31.21 2.74
2913 5881 6.156748 TGCTGAATGGTAATCGTACACTAT 57.843 37.500 0.00 0.00 31.21 2.12
2987 5955 2.290323 CCTTCCATGTTCCTTTCCGAGT 60.290 50.000 0.00 0.00 0.00 4.18
2988 5956 2.762535 TCCATGTTCCTTTCCGAGTC 57.237 50.000 0.00 0.00 0.00 3.36
3015 5987 5.529060 GTCTCATTCAGAAAGAACACACCTT 59.471 40.000 0.00 0.00 39.49 3.50
3108 6081 1.671979 TGCATATGAAGCAGGAGCAC 58.328 50.000 6.97 0.00 45.49 4.40
3140 6113 1.312815 CGCTCCTTCCATGGGAAATC 58.687 55.000 13.02 0.00 41.54 2.17
3252 6225 5.879223 GGATACATCATATTTCTCCCTGCAG 59.121 44.000 6.78 6.78 0.00 4.41
3253 6226 4.785346 ACATCATATTTCTCCCTGCAGT 57.215 40.909 13.81 0.00 0.00 4.40
3254 6227 5.121380 ACATCATATTTCTCCCTGCAGTT 57.879 39.130 13.81 0.00 0.00 3.16
3255 6228 4.885907 ACATCATATTTCTCCCTGCAGTTG 59.114 41.667 13.81 3.36 0.00 3.16
3256 6229 3.282021 TCATATTTCTCCCTGCAGTTGC 58.718 45.455 13.81 0.00 42.50 4.17
3257 6230 2.128771 TATTTCTCCCTGCAGTTGCC 57.871 50.000 13.81 0.00 41.18 4.52
3258 6231 0.112995 ATTTCTCCCTGCAGTTGCCA 59.887 50.000 13.81 0.00 41.18 4.92
3259 6232 0.538057 TTTCTCCCTGCAGTTGCCAG 60.538 55.000 13.81 0.79 41.18 4.85
3260 6233 1.708993 TTCTCCCTGCAGTTGCCAGT 61.709 55.000 13.81 0.00 41.18 4.00
3261 6234 1.970114 CTCCCTGCAGTTGCCAGTG 60.970 63.158 13.81 0.00 41.18 3.66
3262 6235 2.203394 CCCTGCAGTTGCCAGTGT 60.203 61.111 13.81 0.00 41.18 3.55
3263 6236 2.558286 CCCTGCAGTTGCCAGTGTG 61.558 63.158 13.81 0.00 41.18 3.82
3264 6237 2.558286 CCTGCAGTTGCCAGTGTGG 61.558 63.158 13.81 0.00 41.55 4.17
3265 6238 1.526686 CTGCAGTTGCCAGTGTGGA 60.527 57.895 5.25 0.00 40.96 4.02
3266 6239 1.512996 CTGCAGTTGCCAGTGTGGAG 61.513 60.000 5.25 0.00 40.96 3.86
3267 6240 2.912624 GCAGTTGCCAGTGTGGAGC 61.913 63.158 0.00 0.00 40.96 4.70
3268 6241 2.113986 AGTTGCCAGTGTGGAGCC 59.886 61.111 0.00 0.00 40.96 4.70
3269 6242 2.113986 GTTGCCAGTGTGGAGCCT 59.886 61.111 0.00 0.00 40.96 4.58
3270 6243 1.529244 GTTGCCAGTGTGGAGCCTT 60.529 57.895 0.00 0.00 40.96 4.35
3271 6244 1.529010 TTGCCAGTGTGGAGCCTTG 60.529 57.895 0.00 0.00 40.96 3.61
3272 6245 3.368571 GCCAGTGTGGAGCCTTGC 61.369 66.667 0.00 0.00 40.96 4.01
3273 6246 2.674380 CCAGTGTGGAGCCTTGCC 60.674 66.667 0.00 0.00 40.96 4.52
3274 6247 2.113774 CAGTGTGGAGCCTTGCCA 59.886 61.111 0.00 0.00 0.00 4.92
3275 6248 1.970114 CAGTGTGGAGCCTTGCCAG 60.970 63.158 0.00 0.00 35.77 4.85
3276 6249 2.113986 GTGTGGAGCCTTGCCAGT 59.886 61.111 0.00 0.00 35.77 4.00
3277 6250 2.113774 TGTGGAGCCTTGCCAGTG 59.886 61.111 0.00 0.00 35.77 3.66
3278 6251 2.113986 GTGGAGCCTTGCCAGTGT 59.886 61.111 0.00 0.00 35.77 3.55
3279 6252 2.113774 TGGAGCCTTGCCAGTGTG 59.886 61.111 0.00 0.00 0.00 3.82
3280 6253 2.113986 GGAGCCTTGCCAGTGTGT 59.886 61.111 0.00 0.00 0.00 3.72
3281 6254 2.263741 GGAGCCTTGCCAGTGTGTG 61.264 63.158 0.00 0.00 0.00 3.82
3282 6255 1.526917 GAGCCTTGCCAGTGTGTGT 60.527 57.895 0.00 0.00 0.00 3.72
3283 6256 1.076777 AGCCTTGCCAGTGTGTGTT 60.077 52.632 0.00 0.00 0.00 3.32
3284 6257 0.182537 AGCCTTGCCAGTGTGTGTTA 59.817 50.000 0.00 0.00 0.00 2.41
3285 6258 0.310854 GCCTTGCCAGTGTGTGTTAC 59.689 55.000 0.00 0.00 0.00 2.50
3286 6259 0.951558 CCTTGCCAGTGTGTGTTACC 59.048 55.000 0.00 0.00 0.00 2.85
3287 6260 1.476833 CCTTGCCAGTGTGTGTTACCT 60.477 52.381 0.00 0.00 0.00 3.08
3288 6261 2.297701 CTTGCCAGTGTGTGTTACCTT 58.702 47.619 0.00 0.00 0.00 3.50
3289 6262 1.961793 TGCCAGTGTGTGTTACCTTC 58.038 50.000 0.00 0.00 0.00 3.46
3290 6263 1.488812 TGCCAGTGTGTGTTACCTTCT 59.511 47.619 0.00 0.00 0.00 2.85
3291 6264 2.143925 GCCAGTGTGTGTTACCTTCTC 58.856 52.381 0.00 0.00 0.00 2.87
3292 6265 2.224305 GCCAGTGTGTGTTACCTTCTCT 60.224 50.000 0.00 0.00 0.00 3.10
3293 6266 3.006537 GCCAGTGTGTGTTACCTTCTCTA 59.993 47.826 0.00 0.00 0.00 2.43
3294 6267 4.557205 CCAGTGTGTGTTACCTTCTCTAC 58.443 47.826 0.00 0.00 0.00 2.59
3295 6268 4.557205 CAGTGTGTGTTACCTTCTCTACC 58.443 47.826 0.00 0.00 0.00 3.18
3296 6269 4.038763 CAGTGTGTGTTACCTTCTCTACCA 59.961 45.833 0.00 0.00 0.00 3.25
3297 6270 4.038883 AGTGTGTGTTACCTTCTCTACCAC 59.961 45.833 0.00 0.00 0.00 4.16
3298 6271 3.962063 TGTGTGTTACCTTCTCTACCACA 59.038 43.478 0.00 0.00 0.00 4.17
3299 6272 4.038763 TGTGTGTTACCTTCTCTACCACAG 59.961 45.833 0.00 0.00 0.00 3.66
3300 6273 4.038883 GTGTGTTACCTTCTCTACCACAGT 59.961 45.833 0.00 0.00 0.00 3.55
3301 6274 4.652421 TGTGTTACCTTCTCTACCACAGTT 59.348 41.667 0.00 0.00 0.00 3.16
3302 6275 4.989168 GTGTTACCTTCTCTACCACAGTTG 59.011 45.833 0.00 0.00 0.00 3.16
3303 6276 4.652421 TGTTACCTTCTCTACCACAGTTGT 59.348 41.667 0.00 0.00 0.00 3.32
3304 6277 5.129815 TGTTACCTTCTCTACCACAGTTGTT 59.870 40.000 0.00 0.00 0.00 2.83
3305 6278 4.772886 ACCTTCTCTACCACAGTTGTTT 57.227 40.909 0.00 0.00 0.00 2.83
3306 6279 5.112129 ACCTTCTCTACCACAGTTGTTTT 57.888 39.130 0.00 0.00 0.00 2.43
3307 6280 5.123936 ACCTTCTCTACCACAGTTGTTTTC 58.876 41.667 0.00 0.00 0.00 2.29
3308 6281 5.104485 ACCTTCTCTACCACAGTTGTTTTCT 60.104 40.000 0.00 0.00 0.00 2.52
3309 6282 5.823045 CCTTCTCTACCACAGTTGTTTTCTT 59.177 40.000 0.00 0.00 0.00 2.52
3310 6283 6.017852 CCTTCTCTACCACAGTTGTTTTCTTC 60.018 42.308 0.00 0.00 0.00 2.87
3311 6284 5.365619 TCTCTACCACAGTTGTTTTCTTCC 58.634 41.667 0.00 0.00 0.00 3.46
3312 6285 4.457466 TCTACCACAGTTGTTTTCTTCCC 58.543 43.478 0.00 0.00 0.00 3.97
3313 6286 2.021457 ACCACAGTTGTTTTCTTCCCG 58.979 47.619 0.00 0.00 0.00 5.14
3314 6287 2.294074 CCACAGTTGTTTTCTTCCCGA 58.706 47.619 0.00 0.00 0.00 5.14
3315 6288 2.884639 CCACAGTTGTTTTCTTCCCGAT 59.115 45.455 0.00 0.00 0.00 4.18
3316 6289 3.304659 CCACAGTTGTTTTCTTCCCGATG 60.305 47.826 0.00 0.00 0.00 3.84
3317 6290 3.563808 CACAGTTGTTTTCTTCCCGATGA 59.436 43.478 0.00 0.00 0.00 2.92
3318 6291 3.564225 ACAGTTGTTTTCTTCCCGATGAC 59.436 43.478 0.00 0.00 0.00 3.06
3319 6292 3.815401 CAGTTGTTTTCTTCCCGATGACT 59.185 43.478 0.00 0.00 0.00 3.41
3320 6293 4.065789 AGTTGTTTTCTTCCCGATGACTC 58.934 43.478 0.00 0.00 0.00 3.36
3321 6294 3.053831 TGTTTTCTTCCCGATGACTCC 57.946 47.619 0.00 0.00 0.00 3.85
3322 6295 2.370519 TGTTTTCTTCCCGATGACTCCA 59.629 45.455 0.00 0.00 0.00 3.86
3323 6296 3.181449 TGTTTTCTTCCCGATGACTCCAA 60.181 43.478 0.00 0.00 0.00 3.53
3324 6297 2.762535 TTCTTCCCGATGACTCCAAC 57.237 50.000 0.00 0.00 0.00 3.77
3325 6298 0.530744 TCTTCCCGATGACTCCAACG 59.469 55.000 0.00 0.00 38.15 4.10
3329 6302 4.094684 CGATGACTCCAACGGCTC 57.905 61.111 0.00 0.00 35.33 4.70
3330 6303 1.513158 CGATGACTCCAACGGCTCT 59.487 57.895 0.00 0.00 35.33 4.09
3331 6304 0.803768 CGATGACTCCAACGGCTCTG 60.804 60.000 0.00 0.00 35.33 3.35
3332 6305 0.460987 GATGACTCCAACGGCTCTGG 60.461 60.000 0.00 0.00 35.05 3.86
3333 6306 1.194781 ATGACTCCAACGGCTCTGGT 61.195 55.000 2.14 0.00 35.30 4.00
3334 6307 1.374758 GACTCCAACGGCTCTGGTG 60.375 63.158 2.14 2.69 35.30 4.17
3335 6308 2.743928 CTCCAACGGCTCTGGTGC 60.744 66.667 2.14 0.00 35.30 5.01
3336 6309 4.680237 TCCAACGGCTCTGGTGCG 62.680 66.667 2.14 0.00 35.30 5.34
3338 6311 4.988598 CAACGGCTCTGGTGCGGT 62.989 66.667 2.83 2.83 46.02 5.68
3339 6312 4.681978 AACGGCTCTGGTGCGGTC 62.682 66.667 7.95 0.00 43.89 4.79
3342 6315 4.767255 GGCTCTGGTGCGGTCTGG 62.767 72.222 0.00 0.00 0.00 3.86
3403 6376 4.821589 GGCCAAGGCGACTCGGAG 62.822 72.222 0.00 2.83 36.22 4.63
3404 6377 4.821589 GCCAAGGCGACTCGGAGG 62.822 72.222 0.00 0.00 36.22 4.30
3405 6378 4.821589 CCAAGGCGACTCGGAGGC 62.822 72.222 10.23 5.16 36.22 4.70
3502 6475 3.309582 TGGTCGGGGAGCAGATTC 58.690 61.111 0.00 0.00 35.04 2.52
3503 6476 1.306141 TGGTCGGGGAGCAGATTCT 60.306 57.895 0.00 0.00 35.04 2.40
3504 6477 1.144936 GGTCGGGGAGCAGATTCTG 59.855 63.158 9.40 9.40 34.12 3.02
3505 6478 1.144936 GTCGGGGAGCAGATTCTGG 59.855 63.158 15.28 0.00 31.21 3.86
3506 6479 2.066393 TCGGGGAGCAGATTCTGGG 61.066 63.158 15.28 0.00 31.21 4.45
3507 6480 2.194326 GGGGAGCAGATTCTGGGC 59.806 66.667 15.28 1.92 31.21 5.36
3508 6481 2.203126 GGGAGCAGATTCTGGGCG 60.203 66.667 15.28 0.00 31.21 6.13
3509 6482 2.586792 GGAGCAGATTCTGGGCGT 59.413 61.111 15.28 0.00 31.21 5.68
3510 6483 1.078143 GGAGCAGATTCTGGGCGTT 60.078 57.895 15.28 0.00 31.21 4.84
3511 6484 1.372087 GGAGCAGATTCTGGGCGTTG 61.372 60.000 15.28 0.00 31.21 4.10
3512 6485 1.372087 GAGCAGATTCTGGGCGTTGG 61.372 60.000 15.28 0.00 31.21 3.77
3513 6486 3.056313 GCAGATTCTGGGCGTTGGC 62.056 63.158 15.28 0.00 33.01 4.52
3514 6487 1.377725 CAGATTCTGGGCGTTGGCT 60.378 57.895 5.73 0.00 39.81 4.75
3515 6488 1.377725 AGATTCTGGGCGTTGGCTG 60.378 57.895 0.00 0.00 39.81 4.85
3516 6489 1.377202 GATTCTGGGCGTTGGCTGA 60.377 57.895 0.00 0.00 39.81 4.26
3517 6490 1.372087 GATTCTGGGCGTTGGCTGAG 61.372 60.000 0.00 0.00 39.81 3.35
3518 6491 2.826777 ATTCTGGGCGTTGGCTGAGG 62.827 60.000 0.00 0.00 39.81 3.86
3519 6492 4.335647 CTGGGCGTTGGCTGAGGT 62.336 66.667 0.00 0.00 39.81 3.85
3520 6493 2.925706 TGGGCGTTGGCTGAGGTA 60.926 61.111 0.00 0.00 39.81 3.08
3521 6494 2.349755 GGGCGTTGGCTGAGGTAA 59.650 61.111 0.00 0.00 39.81 2.85
3522 6495 1.745489 GGGCGTTGGCTGAGGTAAG 60.745 63.158 0.00 0.00 39.81 2.34
3523 6496 1.003718 GGCGTTGGCTGAGGTAAGT 60.004 57.895 0.00 0.00 39.81 2.24
3524 6497 1.298859 GGCGTTGGCTGAGGTAAGTG 61.299 60.000 0.00 0.00 39.81 3.16
3525 6498 0.320421 GCGTTGGCTGAGGTAAGTGA 60.320 55.000 0.00 0.00 35.83 3.41
3526 6499 1.676014 GCGTTGGCTGAGGTAAGTGAT 60.676 52.381 0.00 0.00 35.83 3.06
3527 6500 2.002586 CGTTGGCTGAGGTAAGTGATG 58.997 52.381 0.00 0.00 0.00 3.07
3528 6501 2.359900 GTTGGCTGAGGTAAGTGATGG 58.640 52.381 0.00 0.00 0.00 3.51
3529 6502 0.253044 TGGCTGAGGTAAGTGATGGC 59.747 55.000 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.871238 CACCTATTTATGTACTGTGTACTTTCT 57.129 33.333 8.94 0.00 0.00 2.52
1 2 9.095065 CCACCTATTTATGTACTGTGTACTTTC 57.905 37.037 8.94 0.00 0.00 2.62
10 11 6.697019 GCATTTTGCCACCTATTTATGTACTG 59.303 38.462 0.00 0.00 37.42 2.74
44 45 0.972134 TCTCTGTGAGAGGGCAAGTG 59.028 55.000 0.83 0.00 42.54 3.16
145 146 6.484643 ACCTCATTCTGGACGATATCAAAATG 59.515 38.462 3.12 3.64 0.00 2.32
198 203 7.189512 ACGAAACAGAAGAGTTTTTGAGAATG 58.810 34.615 0.00 0.00 41.48 2.67
207 212 4.575236 GGAAGGAACGAAACAGAAGAGTTT 59.425 41.667 0.00 0.00 43.90 2.66
211 216 3.830744 TGGAAGGAACGAAACAGAAGA 57.169 42.857 0.00 0.00 0.00 2.87
307 319 5.291178 TGCAAATTCAGTTTCAGATTGGTG 58.709 37.500 0.00 0.00 0.00 4.17
309 321 5.775686 TCTGCAAATTCAGTTTCAGATTGG 58.224 37.500 0.00 0.00 33.27 3.16
342 354 5.391310 CCATACAAGTGACAAGATCTGCAAC 60.391 44.000 0.00 0.00 0.00 4.17
359 371 4.726035 TTTCCAGGGTACAACCATACAA 57.274 40.909 0.00 0.00 41.02 2.41
360 372 4.351407 TCTTTTCCAGGGTACAACCATACA 59.649 41.667 0.00 0.00 41.02 2.29
361 373 4.913784 TCTTTTCCAGGGTACAACCATAC 58.086 43.478 0.00 0.00 41.02 2.39
362 374 5.586155 TTCTTTTCCAGGGTACAACCATA 57.414 39.130 0.00 0.00 41.02 2.74
363 375 4.463050 TTCTTTTCCAGGGTACAACCAT 57.537 40.909 0.00 0.00 41.02 3.55
364 376 3.955524 TTCTTTTCCAGGGTACAACCA 57.044 42.857 0.00 0.00 41.02 3.67
365 377 3.319972 GGTTTCTTTTCCAGGGTACAACC 59.680 47.826 0.00 0.00 37.60 3.77
366 378 3.955551 TGGTTTCTTTTCCAGGGTACAAC 59.044 43.478 0.00 0.00 0.00 3.32
376 388 4.023963 CGAGAGAGGTTTGGTTTCTTTTCC 60.024 45.833 0.00 0.00 0.00 3.13
405 417 1.267982 GCATATCACGTTGCGATGCAA 60.268 47.619 13.70 0.00 46.80 4.08
438 450 1.493950 CGATTGTGCGATCAGGAGCC 61.494 60.000 0.00 0.00 0.00 4.70
440 452 1.203928 GTCGATTGTGCGATCAGGAG 58.796 55.000 0.00 0.00 42.82 3.69
454 466 1.536766 CACACAATGCCTGTTGTCGAT 59.463 47.619 0.00 0.00 40.17 3.59
628 653 7.526041 ACTTGCCAAACCATTATATATGGAGA 58.474 34.615 16.26 0.00 41.64 3.71
750 775 6.410914 CGTATTTTAAGAGCCACGCTATTTTG 59.589 38.462 0.00 0.00 36.68 2.44
757 782 2.086934 GCGTATTTTAAGAGCCACGC 57.913 50.000 0.92 0.92 46.31 5.34
764 789 7.429636 AGCACACTAAAAGCGTATTTTAAGA 57.570 32.000 8.41 0.00 0.00 2.10
771 796 5.345202 GCGATATAGCACACTAAAAGCGTAT 59.655 40.000 2.59 0.00 32.76 3.06
813 838 4.966965 AGATCAGAATACAACGTCTCGT 57.033 40.909 0.00 0.00 43.97 4.18
815 840 8.907685 GCTAAATAGATCAGAATACAACGTCTC 58.092 37.037 0.00 0.00 0.00 3.36
827 852 5.923114 GCAATGTCTCGCTAAATAGATCAGA 59.077 40.000 0.00 0.00 0.00 3.27
867 892 4.499758 GCACTATTGAGTCGCTAACAGTAC 59.500 45.833 0.00 0.00 31.73 2.73
872 897 2.527100 ACGCACTATTGAGTCGCTAAC 58.473 47.619 0.00 0.00 31.73 2.34
875 900 2.933495 TAACGCACTATTGAGTCGCT 57.067 45.000 0.00 0.00 34.18 4.93
902 927 7.232994 CGGGTTTTGCAACATTATAAACAATG 58.767 34.615 0.00 0.00 40.93 2.82
903 928 6.128418 GCGGGTTTTGCAACATTATAAACAAT 60.128 34.615 0.00 0.00 34.15 2.71
960 987 2.798445 TAGCCTGCCTGAGACCGGAA 62.798 60.000 9.46 0.00 0.00 4.30
1249 1279 0.249868 GGTGCCCAAAAAGAAGCCAC 60.250 55.000 0.00 0.00 0.00 5.01
1520 4442 3.838271 GATGCCCGGTCGAGCTCA 61.838 66.667 15.40 8.16 0.00 4.26
1590 4524 1.622811 GGCATCATACCTAGAGCAGCT 59.377 52.381 0.00 0.00 0.00 4.24
1601 4535 6.509418 TTTTAAGGACTTGTGGCATCATAC 57.491 37.500 0.00 0.00 0.00 2.39
1710 4659 3.443099 TCATACATCAGACCAAGCTCG 57.557 47.619 0.00 0.00 0.00 5.03
1891 4840 2.017049 CAGGAAAAGGCCACCGATAAG 58.983 52.381 5.01 0.00 0.00 1.73
2015 4964 1.202806 CCGGCCATCCAATATCACTGT 60.203 52.381 2.24 0.00 0.00 3.55
2276 5240 3.587797 TTACTTCACTGGCTAAGACCG 57.412 47.619 0.00 0.00 0.00 4.79
2317 5281 2.181975 AGGTTCAAGATTGGGCCAATG 58.818 47.619 35.23 22.73 33.90 2.82
2413 5381 4.095483 AGTTTGTTGTTCACTCAAGAGCAG 59.905 41.667 0.00 0.00 30.36 4.24
2496 5464 1.109609 ATTCCGAACGGAGGGAGTAC 58.890 55.000 15.34 0.00 46.06 2.73
2497 5465 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
2498 5466 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
2499 5467 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
2500 5468 1.753073 GAGTAATTCCGAACGGAGGGA 59.247 52.381 15.34 2.49 46.06 4.20
2501 5469 1.535437 CGAGTAATTCCGAACGGAGGG 60.535 57.143 15.34 0.00 46.06 4.30
2502 5470 1.133790 ACGAGTAATTCCGAACGGAGG 59.866 52.381 15.34 4.28 46.06 4.30
2503 5471 2.448219 GACGAGTAATTCCGAACGGAG 58.552 52.381 15.34 5.60 46.06 4.63
2504 5472 1.133025 GGACGAGTAATTCCGAACGGA 59.867 52.381 12.04 12.04 43.52 4.69
2505 5473 1.135315 TGGACGAGTAATTCCGAACGG 60.135 52.381 6.94 6.94 0.00 4.44
2506 5474 2.267188 TGGACGAGTAATTCCGAACG 57.733 50.000 0.00 0.00 0.00 3.95
2507 5475 6.651755 TTTATTGGACGAGTAATTCCGAAC 57.348 37.500 0.00 0.00 0.00 3.95
2508 5476 7.042950 TCATTTATTGGACGAGTAATTCCGAA 58.957 34.615 0.00 0.00 0.00 4.30
2509 5477 6.575267 TCATTTATTGGACGAGTAATTCCGA 58.425 36.000 0.00 0.00 0.00 4.55
2510 5478 6.838198 TCATTTATTGGACGAGTAATTCCG 57.162 37.500 0.00 0.00 0.00 4.30
2511 5479 8.621286 ACATTCATTTATTGGACGAGTAATTCC 58.379 33.333 0.00 0.00 0.00 3.01
2517 5485 9.698309 CTAGATACATTCATTTATTGGACGAGT 57.302 33.333 0.00 0.00 0.00 4.18
2518 5486 9.914131 TCTAGATACATTCATTTATTGGACGAG 57.086 33.333 0.00 0.00 0.00 4.18
2579 5547 9.296400 CCGTTCGGAATTATTTATCACAAAAAT 57.704 29.630 5.19 0.00 0.00 1.82
2580 5548 8.512956 TCCGTTCGGAATTATTTATCACAAAAA 58.487 29.630 11.66 0.00 0.00 1.94
2581 5549 8.041829 TCCGTTCGGAATTATTTATCACAAAA 57.958 30.769 11.66 0.00 0.00 2.44
2582 5550 7.201661 CCTCCGTTCGGAATTATTTATCACAAA 60.202 37.037 14.79 0.00 33.41 2.83
2583 5551 6.259167 CCTCCGTTCGGAATTATTTATCACAA 59.741 38.462 14.79 0.00 33.41 3.33
2584 5552 5.756347 CCTCCGTTCGGAATTATTTATCACA 59.244 40.000 14.79 0.00 33.41 3.58
2585 5553 5.178809 CCCTCCGTTCGGAATTATTTATCAC 59.821 44.000 14.79 0.00 33.41 3.06
2586 5554 5.070714 TCCCTCCGTTCGGAATTATTTATCA 59.929 40.000 14.79 0.00 33.41 2.15
2587 5555 5.544650 TCCCTCCGTTCGGAATTATTTATC 58.455 41.667 14.79 0.00 33.41 1.75
2588 5556 5.071384 ACTCCCTCCGTTCGGAATTATTTAT 59.929 40.000 14.79 0.00 33.41 1.40
2589 5557 4.406649 ACTCCCTCCGTTCGGAATTATTTA 59.593 41.667 14.79 0.00 33.41 1.40
2590 5558 3.199289 ACTCCCTCCGTTCGGAATTATTT 59.801 43.478 14.79 0.00 33.41 1.40
2591 5559 2.770232 ACTCCCTCCGTTCGGAATTATT 59.230 45.455 14.79 0.00 33.41 1.40
2592 5560 2.395619 ACTCCCTCCGTTCGGAATTAT 58.604 47.619 14.79 0.00 33.41 1.28
2593 5561 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2594 5562 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
2595 5563 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
2596 5564 0.967380 GGTACTCCCTCCGTTCGGAA 60.967 60.000 14.79 0.04 33.41 4.30
2597 5565 1.379044 GGTACTCCCTCCGTTCGGA 60.379 63.158 13.34 13.34 0.00 4.55
2598 5566 1.379576 AGGTACTCCCTCCGTTCGG 60.380 63.158 4.74 4.74 40.71 4.30
2599 5567 4.333417 AGGTACTCCCTCCGTTCG 57.667 61.111 0.00 0.00 40.71 3.95
2672 5640 2.266554 CTCTGGCGAATGAGAGTTCAC 58.733 52.381 0.00 0.00 35.83 3.18
2717 5685 1.067354 GGTTGGACGTCGGACACTATT 60.067 52.381 17.96 0.00 0.00 1.73
2726 5694 2.317609 CCTTGCTGGTTGGACGTCG 61.318 63.158 9.92 0.00 0.00 5.12
2736 5704 4.085876 CCAGTGTTCCCTTGCTGG 57.914 61.111 0.00 0.00 41.89 4.85
2739 5707 0.322008 CTCCTCCAGTGTTCCCTTGC 60.322 60.000 0.00 0.00 0.00 4.01
2794 5762 4.021925 ACCTCTGACTTGCCGGCC 62.022 66.667 26.77 9.02 0.00 6.13
2807 5775 1.448540 CCACATGCGACTCCACCTC 60.449 63.158 0.00 0.00 0.00 3.85
2885 5853 2.238646 ACGATTACCATTCAGCAAGGGA 59.761 45.455 0.00 0.00 36.89 4.20
2886 5854 2.643551 ACGATTACCATTCAGCAAGGG 58.356 47.619 0.00 0.00 39.55 3.95
2887 5855 4.034048 GTGTACGATTACCATTCAGCAAGG 59.966 45.833 0.00 0.00 0.00 3.61
2890 5858 4.465632 AGTGTACGATTACCATTCAGCA 57.534 40.909 0.00 0.00 0.00 4.41
2892 5860 8.107399 TCCTATAGTGTACGATTACCATTCAG 57.893 38.462 0.00 0.00 0.00 3.02
2893 5861 8.645814 ATCCTATAGTGTACGATTACCATTCA 57.354 34.615 0.00 0.00 0.00 2.57
2920 5888 7.558604 ACAGCTGCATCAAAATTGGTAATTAT 58.441 30.769 15.27 0.00 0.00 1.28
2987 5955 3.323691 TGTTCTTTCTGAATGAGACGGGA 59.676 43.478 6.17 0.00 36.99 5.14
2988 5956 3.433615 GTGTTCTTTCTGAATGAGACGGG 59.566 47.826 6.17 0.00 36.99 5.28
3140 6113 6.631962 TCATATAGCAGATCATCAGCTTCAG 58.368 40.000 10.19 0.00 39.93 3.02
3168 6141 8.417273 TCATGCATGGAGAAATATGATGAAAT 57.583 30.769 25.97 0.00 0.00 2.17
3252 6225 1.529244 AAGGCTCCACACTGGCAAC 60.529 57.895 0.00 0.00 37.47 4.17
3253 6226 1.529010 CAAGGCTCCACACTGGCAA 60.529 57.895 0.00 0.00 37.47 4.52
3254 6227 2.113774 CAAGGCTCCACACTGGCA 59.886 61.111 0.00 0.00 37.47 4.92
3255 6228 3.368571 GCAAGGCTCCACACTGGC 61.369 66.667 0.00 0.00 37.47 4.85
3256 6229 2.674380 GGCAAGGCTCCACACTGG 60.674 66.667 0.00 0.00 39.43 4.00
3257 6230 1.970114 CTGGCAAGGCTCCACACTG 60.970 63.158 0.00 0.00 0.00 3.66
3258 6231 2.433446 CTGGCAAGGCTCCACACT 59.567 61.111 0.00 0.00 0.00 3.55
3259 6232 2.113986 ACTGGCAAGGCTCCACAC 59.886 61.111 0.00 0.00 0.00 3.82
3260 6233 2.113774 CACTGGCAAGGCTCCACA 59.886 61.111 0.00 0.00 0.00 4.17
3261 6234 2.113986 ACACTGGCAAGGCTCCAC 59.886 61.111 0.00 0.00 0.00 4.02
3262 6235 2.113774 CACACTGGCAAGGCTCCA 59.886 61.111 0.00 0.00 0.00 3.86
3263 6236 2.113986 ACACACTGGCAAGGCTCC 59.886 61.111 0.00 0.00 0.00 4.70
3264 6237 1.103398 AACACACACTGGCAAGGCTC 61.103 55.000 0.00 0.00 0.00 4.70
3265 6238 0.182537 TAACACACACTGGCAAGGCT 59.817 50.000 0.00 0.00 0.00 4.58
3266 6239 0.310854 GTAACACACACTGGCAAGGC 59.689 55.000 0.00 0.00 0.00 4.35
3267 6240 0.951558 GGTAACACACACTGGCAAGG 59.048 55.000 0.00 0.00 0.00 3.61
3268 6241 1.967319 AGGTAACACACACTGGCAAG 58.033 50.000 0.00 0.00 41.41 4.01
3269 6242 2.092646 AGAAGGTAACACACACTGGCAA 60.093 45.455 0.00 0.00 41.41 4.52
3270 6243 1.488812 AGAAGGTAACACACACTGGCA 59.511 47.619 0.00 0.00 41.41 4.92
3271 6244 2.143925 GAGAAGGTAACACACACTGGC 58.856 52.381 0.00 0.00 41.41 4.85
3272 6245 3.753294 AGAGAAGGTAACACACACTGG 57.247 47.619 0.00 0.00 41.41 4.00
3273 6246 4.038763 TGGTAGAGAAGGTAACACACACTG 59.961 45.833 0.00 0.00 41.41 3.66
3274 6247 4.038883 GTGGTAGAGAAGGTAACACACACT 59.961 45.833 0.00 0.00 37.91 3.55
3275 6248 4.202182 TGTGGTAGAGAAGGTAACACACAC 60.202 45.833 0.00 0.00 42.00 3.82
3276 6249 3.962063 TGTGGTAGAGAAGGTAACACACA 59.038 43.478 0.00 0.00 42.00 3.72
3277 6250 4.038883 ACTGTGGTAGAGAAGGTAACACAC 59.961 45.833 0.00 0.00 42.00 3.82
3278 6251 4.220724 ACTGTGGTAGAGAAGGTAACACA 58.779 43.478 1.34 1.34 44.11 3.72
3279 6252 4.868314 ACTGTGGTAGAGAAGGTAACAC 57.132 45.455 0.00 0.00 38.39 3.32
3280 6253 4.652421 ACAACTGTGGTAGAGAAGGTAACA 59.348 41.667 0.00 0.00 41.41 2.41
3281 6254 5.211174 ACAACTGTGGTAGAGAAGGTAAC 57.789 43.478 0.00 0.00 0.00 2.50
3282 6255 5.881923 AACAACTGTGGTAGAGAAGGTAA 57.118 39.130 0.00 0.00 0.00 2.85
3283 6256 5.881923 AAACAACTGTGGTAGAGAAGGTA 57.118 39.130 0.00 0.00 0.00 3.08
3284 6257 4.772886 AAACAACTGTGGTAGAGAAGGT 57.227 40.909 0.00 0.00 0.00 3.50
3285 6258 5.368989 AGAAAACAACTGTGGTAGAGAAGG 58.631 41.667 0.00 0.00 0.00 3.46
3286 6259 6.017852 GGAAGAAAACAACTGTGGTAGAGAAG 60.018 42.308 0.00 0.00 0.00 2.85
3287 6260 5.820947 GGAAGAAAACAACTGTGGTAGAGAA 59.179 40.000 0.00 0.00 0.00 2.87
3288 6261 5.365619 GGAAGAAAACAACTGTGGTAGAGA 58.634 41.667 0.00 0.00 0.00 3.10
3289 6262 4.515567 GGGAAGAAAACAACTGTGGTAGAG 59.484 45.833 0.00 0.00 0.00 2.43
3290 6263 4.457466 GGGAAGAAAACAACTGTGGTAGA 58.543 43.478 0.00 0.00 0.00 2.59
3291 6264 3.250040 CGGGAAGAAAACAACTGTGGTAG 59.750 47.826 0.00 0.00 0.00 3.18
3292 6265 3.118334 TCGGGAAGAAAACAACTGTGGTA 60.118 43.478 0.00 0.00 0.00 3.25
3293 6266 2.021457 CGGGAAGAAAACAACTGTGGT 58.979 47.619 0.00 0.00 0.00 4.16
3294 6267 2.294074 TCGGGAAGAAAACAACTGTGG 58.706 47.619 0.00 0.00 0.00 4.17
3295 6268 3.563808 TCATCGGGAAGAAAACAACTGTG 59.436 43.478 0.00 0.00 0.00 3.66
3296 6269 3.564225 GTCATCGGGAAGAAAACAACTGT 59.436 43.478 0.00 0.00 0.00 3.55
3297 6270 3.815401 AGTCATCGGGAAGAAAACAACTG 59.185 43.478 0.00 0.00 0.00 3.16
3298 6271 4.065789 GAGTCATCGGGAAGAAAACAACT 58.934 43.478 0.00 0.00 0.00 3.16
3299 6272 3.188667 GGAGTCATCGGGAAGAAAACAAC 59.811 47.826 0.00 0.00 0.00 3.32
3300 6273 3.181449 TGGAGTCATCGGGAAGAAAACAA 60.181 43.478 0.00 0.00 0.00 2.83
3301 6274 2.370519 TGGAGTCATCGGGAAGAAAACA 59.629 45.455 0.00 0.00 0.00 2.83
3302 6275 3.053831 TGGAGTCATCGGGAAGAAAAC 57.946 47.619 0.00 0.00 0.00 2.43
3303 6276 3.408634 GTTGGAGTCATCGGGAAGAAAA 58.591 45.455 0.00 0.00 0.00 2.29
3304 6277 2.611971 CGTTGGAGTCATCGGGAAGAAA 60.612 50.000 0.00 0.00 33.76 2.52
3305 6278 1.067142 CGTTGGAGTCATCGGGAAGAA 60.067 52.381 0.00 0.00 33.76 2.52
3306 6279 0.530744 CGTTGGAGTCATCGGGAAGA 59.469 55.000 0.00 0.00 33.76 2.87
3307 6280 0.460284 CCGTTGGAGTCATCGGGAAG 60.460 60.000 10.61 0.00 46.75 3.46
3308 6281 1.594833 CCGTTGGAGTCATCGGGAA 59.405 57.895 10.61 0.00 46.75 3.97
3309 6282 3.294750 CCGTTGGAGTCATCGGGA 58.705 61.111 10.61 0.00 46.75 5.14
3312 6285 0.803768 CAGAGCCGTTGGAGTCATCG 60.804 60.000 0.00 0.00 36.26 3.84
3313 6286 0.460987 CCAGAGCCGTTGGAGTCATC 60.461 60.000 0.00 0.00 37.96 2.92
3314 6287 1.194781 ACCAGAGCCGTTGGAGTCAT 61.195 55.000 5.81 0.00 39.08 3.06
3315 6288 1.837051 ACCAGAGCCGTTGGAGTCA 60.837 57.895 5.81 0.00 39.08 3.41
3316 6289 1.374758 CACCAGAGCCGTTGGAGTC 60.375 63.158 5.81 0.00 39.08 3.36
3317 6290 2.743718 CACCAGAGCCGTTGGAGT 59.256 61.111 5.81 0.00 39.08 3.85
3318 6291 2.743928 GCACCAGAGCCGTTGGAG 60.744 66.667 5.81 0.00 39.08 3.86
3319 6292 4.680237 CGCACCAGAGCCGTTGGA 62.680 66.667 5.81 0.00 39.08 3.53
3321 6294 4.988598 ACCGCACCAGAGCCGTTG 62.989 66.667 0.00 0.00 0.00 4.10
3322 6295 4.681978 GACCGCACCAGAGCCGTT 62.682 66.667 0.00 0.00 0.00 4.44
3325 6298 4.767255 CCAGACCGCACCAGAGCC 62.767 72.222 0.00 0.00 0.00 4.70
3386 6359 4.821589 CTCCGAGTCGCCTTGGCC 62.822 72.222 7.12 0.00 41.52 5.36
3387 6360 4.821589 CCTCCGAGTCGCCTTGGC 62.822 72.222 7.12 0.75 41.52 4.52
3388 6361 4.821589 GCCTCCGAGTCGCCTTGG 62.822 72.222 7.12 6.97 42.95 3.61
3389 6362 4.821589 GGCCTCCGAGTCGCCTTG 62.822 72.222 7.12 0.00 39.70 3.61
3483 6456 2.932130 GAATCTGCTCCCCGACCAGC 62.932 65.000 0.00 0.00 36.08 4.85
3484 6457 1.144936 GAATCTGCTCCCCGACCAG 59.855 63.158 0.00 0.00 0.00 4.00
3485 6458 1.306141 AGAATCTGCTCCCCGACCA 60.306 57.895 0.00 0.00 0.00 4.02
3486 6459 1.144936 CAGAATCTGCTCCCCGACC 59.855 63.158 0.00 0.00 0.00 4.79
3487 6460 1.144936 CCAGAATCTGCTCCCCGAC 59.855 63.158 4.40 0.00 0.00 4.79
3488 6461 2.066393 CCCAGAATCTGCTCCCCGA 61.066 63.158 4.40 0.00 0.00 5.14
3489 6462 2.507944 CCCAGAATCTGCTCCCCG 59.492 66.667 4.40 0.00 0.00 5.73
3490 6463 2.194326 GCCCAGAATCTGCTCCCC 59.806 66.667 4.40 0.00 0.00 4.81
3491 6464 2.203126 CGCCCAGAATCTGCTCCC 60.203 66.667 4.40 0.00 0.00 4.30
3492 6465 1.078143 AACGCCCAGAATCTGCTCC 60.078 57.895 4.40 0.00 0.00 4.70
3493 6466 1.372087 CCAACGCCCAGAATCTGCTC 61.372 60.000 4.40 0.00 0.00 4.26
3494 6467 1.377725 CCAACGCCCAGAATCTGCT 60.378 57.895 4.40 0.00 0.00 4.24
3495 6468 3.056313 GCCAACGCCCAGAATCTGC 62.056 63.158 4.40 0.00 0.00 4.26
3496 6469 1.377725 AGCCAACGCCCAGAATCTG 60.378 57.895 2.68 2.68 34.57 2.90
3497 6470 1.377725 CAGCCAACGCCCAGAATCT 60.378 57.895 0.00 0.00 34.57 2.40
3498 6471 1.372087 CTCAGCCAACGCCCAGAATC 61.372 60.000 0.00 0.00 34.57 2.52
3499 6472 1.377725 CTCAGCCAACGCCCAGAAT 60.378 57.895 0.00 0.00 34.57 2.40
3500 6473 2.032528 CTCAGCCAACGCCCAGAA 59.967 61.111 0.00 0.00 34.57 3.02
3501 6474 4.020617 CCTCAGCCAACGCCCAGA 62.021 66.667 0.00 0.00 34.57 3.86
3502 6475 2.463589 TTACCTCAGCCAACGCCCAG 62.464 60.000 0.00 0.00 34.57 4.45
3503 6476 2.463589 CTTACCTCAGCCAACGCCCA 62.464 60.000 0.00 0.00 34.57 5.36
3504 6477 1.745489 CTTACCTCAGCCAACGCCC 60.745 63.158 0.00 0.00 34.57 6.13
3505 6478 1.003718 ACTTACCTCAGCCAACGCC 60.004 57.895 0.00 0.00 34.57 5.68
3506 6479 0.320421 TCACTTACCTCAGCCAACGC 60.320 55.000 0.00 0.00 0.00 4.84
3507 6480 2.002586 CATCACTTACCTCAGCCAACG 58.997 52.381 0.00 0.00 0.00 4.10
3508 6481 2.359900 CCATCACTTACCTCAGCCAAC 58.640 52.381 0.00 0.00 0.00 3.77
3509 6482 1.340017 GCCATCACTTACCTCAGCCAA 60.340 52.381 0.00 0.00 0.00 4.52
3510 6483 0.253044 GCCATCACTTACCTCAGCCA 59.747 55.000 0.00 0.00 0.00 4.75
3511 6484 3.086733 GCCATCACTTACCTCAGCC 57.913 57.895 0.00 0.00 0.00 4.85


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.